eggnog-mapper
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eggnogdb
Fast genome-wide functional annotation through orthology assignment
Hi, I have a couple of questions about the eggnog database and eggnog mapper: 1) I would be interested in using an older version of the database, EGGNOG 4.5. Should...
The `distutils` package has been deprecated and is not available in Python 3.12 onwards (https://docs.python.org/3.10/whatsnew/3.10.html#distutils-deprecated), but it is a dependency of eggnog-mapper. The PyPI and Conda recipes currently only specify...
Hi there, I have installed eggnog through conda and I have made a custom database with Drosophilidae proteins to annotate against. To do that I execute: emapper.py --output_dir . -o...
I've encountered an issue with the wrap_up method in the emapper.py script, where the script throws a shutil.SameFileError when the source and destination paths for copying a file are the...
Hello everyone, I apologize for not having much experience in this aspect of analysis. Back in September, I attempted to annotate my total RNA seq data. At that time, I...
Recipe Advice for Annotating Unknown Genes from RNAseq Analysis Using Orthologs from Related Species
Hi everyone, this is not an issue, but I’m looking for some advice on following the recipes you provide in the "_A few recipes_" section of [v2.1.5 to v2.1.12](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.12). A...
Hello. I am using EggNOG-mapper to functionally annotate my genome of an African antelope ~2.9Gb. I used GeMoMa to structurally annotate using 6 different species. GeMoMa produced 29820 gene models...
I'm running eggnog-mapper on a protein fasta file, and I get output in the .hits and .seed_orthologs files, but the .annotations file is empty and says "0 queries scanned." I'm...
Hi, Some descriptions in *.emapper.annotations.tsv contain semicolon e.g.: `Domain in the RNA-binding Lupus La protein; unknown function` The semicolon is transferred to gff in the decoration step, creating a new...
